Influence of 5-bromodeoxycytosine substitution on triplex DNA stability and conformation

Three triple-helical hairpin DNAs with substitution of 5-bromocytosine for cytosine in different strands have been investigated by molecular mechanics and Raman spectroscopy. The stability of the three substituted triplexes w ere compared with the corresponding unsubstituted tripler DNA by the molecu lar mechanics method. Base stacking interactions and strand-strand interact ions of each tripler were analyzed in detail. Sugar conformations in these triplexes have been determined by both vibrational spectroscopy and molecul ar dynamics simulation. The hairpin triplexes with substitution occurring i n strand I or both in strands I and III have the main sugar conformation of CS'-endo, while the tripler with substitution occurring in strand III is t he combination of C3'-endo and C2'-endo sugar conformation. Theoretical res ults are basically in agreement with experiments. (C) 1999 Elsevier Science B.V. All rights reserved.